Foucault's Pendulum is divided into ten segments represented by the ten Sefiroth. The novel is full of esoteric references to Kabbalah, alchemy and conspiracy theory—so many, that critic and novelist Anthony Burgess suggested that it needed an index.[1] The pendulum of the title refers to an actual pendulum designed by the French physicist Léon Foucault to demonstrate Earth's rotation, and has symbolic significance within the novel. Some believe it refers to the philosopher Michel Foucault,[2] noting Eco's friendship with the French philosopher,[3] but the author "specifically rejects any intentional reference to Michel Foucault"[4]—this is regarded as one of his subtle literary jokes.[5]

After reading too many manuscripts about occult conspiracy theories, three vanity publisher employees (Belbo, Diotallevi and Casaubon) invent their own conspiracy for fun. They call this satirical intellectual game "The Plan". The three become increasingly obsessed with The Plan, and sometimes forget that it is just a game. Worse still, other conspiracy theorists learn about The Plan, and take it seriously. Belbo finds himself the target of a real secret society that believes he possesses the key to the lost treasure of the Knights Templar.

The book opens with the narrator, Casaubon (his name refers to classical scholar Isaac Casaubon, and also evokes a scholar character in George Eliot's Middlemarch) hiding in fear after closing time in the Parisian technical museum Musée des Arts et Métiers. He believes that members of a secret society have kidnapped Belbo and are now after him. Most of the novel is then told in flashback as Casaubon waits in the museum.

Casaubon had been a student in 1970s Milan, working on a thesis on the history of the Knights Templar while taking part in the revolutionary and counter-revolutionary activities of the students around him. During this period he meets Belbo, who works as an editor in a publishing house. Belbo invites Casaubon to review the manuscript of a supposedly non-fiction book about the Templars. Casaubon also meets Belbo's colleague Diotallevi, a cabalist.

The book, by a Colonel Ardenti, claims a hidden coded manuscript has revealed a secret plan of the medieval Templars to take over the world. This supposed conspiracy is meant as revenge for the deaths of the Templar leaders when their order was disbanded by the King of France. Ardenti postulates that the Templars were the guardians of a secret treasure, perhaps the Holy Grail of legend, which he suspects was a radioactive energy source.

According to Ardenti's theory, after the French monarchy and the Catholic Church disbanded the Templars on the grounds of heresy, some knights escaped and established cells throughout the world. These cells have been meeting at regular intervals in distinct places to pass on information about the Grail. Ultimately, these cells will reunite to rediscover the Grail's location and achieve world domination. According to Ardenti's calculations, the Templars should have taken over the world in 1944; evidently the plan has been interrupted.

Ardenti mysteriously vanishes after meeting with Belbo and Casaubon to discuss his book. A police inspector, De Angelis, interviews both men. He hints that his job as a political department investigator leads him to investigate not only revolutionaries but also people who claim to be linked to the Occult.

Casaubon has a romance with a Brazilian woman named Amparo. He leaves Italy to follow her and spends a few years in Brazil. While living there, he learns about South American and Caribbean spiritualism, and meets Agliè, an elderly man who implies that he is the mystical Comte de Saint-Germain. Agliè has a seemingly infinite supply of knowledge about things concerning the Occult. While in Brazil, Casaubon receives a letter from Belbo about attending a meeting of occultists. At the meeting Belbo was reminded of the Colonel's conspiracy theory by the words of a young woman who was apparently in a trance. Casaubon and Amparo also attend an occult event in Brazil, an Umbanda rite. During the ritual Amparo falls into a trance herself, an experience she finds deeply disturbing and embarrassing, as she is Marxist by ideology and as such disbelieves and shuns spiritual and religious experiences. Her relationship with Casaubon falls apart, and he returns to Italy.

On his return to Milan, Casaubon begins working as a freelance researcher. At the library he meets a woman named Lia; the two fall in love and eventually have a child together. Meanwhile, Casaubon is hired by Belbo's boss, Mr. Garamond (his name refers to French publisher Claude Garamond), to research illustrations for a history of metals the company is preparing. Casaubon learns that as well as the respectable Garamond publishing house, Mr. Garamond also owns Manuzio, a vanity publisher that charges incompetent authors large sums of money to print their work (rendered "Manutius" in the English translation, a reference to the 15th century printer Aldus Manutius).

Mr. Garamond soon has the idea to begin two lines of occult books: one intended for serious publication by Garamond; the other, Isis Unveiled (a reference to the theosophical text by Blavatsky), to be published by Manutius in order to attract more vanity authors.

Belbo, Diotallevi and Casaubon quickly become submerged in occult manuscripts that draw all sorts of flimsy connections between historical events. They nickname the authors the "Diabolicals", and engage Agliè as a specialist reader.

The three editors start to develop their own conspiracy theory, "The Plan", as part satire and part intellectual game. Starting from Ardenti's "secret manuscript", they develop an intricate web of mystical connections. They also make use of Belbo's small personal computer, which he has nicknamed Abulafia. Belbo mainly uses Abulafia for his personal writings (the novel contains many excerpts of these, discovered by Casaubon as he goes through Abulafia's files), but it came equipped with a small program that can rearrange text in random. (Compare with the game of Dissociated Press and Ramon Llull's Ars Magna.) They use this program to create the "connections" which inspire their Plan. They enter randomly selected words from the Diabolicals' manuscripts, logical operators ("What follows is not true", "If", "Then", etc.), truisms (such as "The Templars have something to do with everything") and "neutral data" (such as "Minnie Mouse is Mickey Mouse's fiancée") and use Abulafia to create new text.

Their first attempt ends up recreating (after a liberal interpretation of the results) the Mary Magdalene conspiracy theory central to The Holy Blood and the Holy Grail. Casaubon jokingly suggests that to create something truly new Belbo must look for occult connections in non-obvious contexts, such as by linking the Kabbalah to a car's spark plugs. (Belbo actually does this, and after some research concludes that the powertrain is a metaphor for the Tree of life.) Pleased with the results of the random text program, the three continue resorting to Abulafia whenever they reach a dead-end with their game.

"The Plan" evolves slowly, but the final version involves the Knights Templar's coming into possession of an ancient secret knowledge of energy flows called telluric currents during the Crusades. The original Knights Templar organization is destroyed after the execution of Jacques de Molay, but the members split into independent cells located in several corners of Europe and the Middle East. As in Ardenti's original theory, each cell is given part of the Templar "Plan" and information about the secret discovery. They are to meet periodically at different locations to share sections of the Plan, gradually reconstructing the original. Then they will reunite and take over the world using the power of the telluric currents. The crucial instruments involved in their plan are a special map and the Foucault pendulum.

While the Plan is far-fetched, the editors become increasingly involved in their game. They even begin to think that there might really be a secret conspiracy after all. Ardenti's disappearance, and his original "coded manuscript", seem to have no other explanation.

However, when Casaubon's girlfriend Lia asks to see the coded manuscript, she comes up with a mundane interpretation. She suggests that the document is simply a delivery list, and encourages Casaubon to abandon the game as she fears it is having a negative effect on him.

When Diotallevi is diagnosed with cancer, he attributes this to his participation in The Plan. He feels that the disease is a divine punishment for involving himself in mysteries he should have left alone and creating a game that mocked something larger than them all. Belbo meanwhile retreats even farther into the Plan to avoid confronting problems in his personal life.

The three had sent Agliè their chronology of secret societies in the Plan, pretending it was not their own work but rather a manuscript they had been presented with. Their list includes historic organizations such as the Templars, Rosicrucians, Paulicians and Synarchists, but they also invent a fictional secret society called the Tres (Templi Resurgentes Equites Synarchici, Latin for "the Risen again Synarchic Knights of the Temple"). The Tres is introduced to trick Agliè. Upon reading the list, he claims not to have heard of the Tres before. (The word was first mentioned to Casaubon by the policeman De Angelis. De Angelis had asked Casaubon if he has ever heard of the Tres.)

Belbo goes to Agliè privately and describes The Plan to him as though it were the result of serious research. He also claims to be in possession of the secret Templar map. Agliè becomes frustrated with Belbo's refusal to let him see this (non-existent) map. He frames Belbo as a terrorist suspect in order to force him to come to Paris. Agliè has cast himself as the head of a secret spiritual brotherhood, which includes Mr. Garamond, Colonel Ardenti and many of the Diabolical authors. Belbo tries to get help from De Angelis, but he has just transferred to Sardinia after an attempted car bombing, and refuses to get involved.

Casaubon receives a call for help; he goes to Belbo's apartment, and reads all the documents that Belbo stored in his computer, then decides to follow Belbo to Paris himself. He decides that Agliè and his associates must intend to meet at the museum where Foucault's Pendulum is housed, as Belbo had claimed that the Templar map had to be used in conjunction with the pendulum. Casaubon hides in the museum, where he was when the novel opened.

At the appointed hour, a group of people gather around the pendulum for an arcane ritual. Casaubon sees several ectoplasmic forms appear, one of which claims to be the real Comte de Saint-Germain and discredits Agliè in front of his followers. Belbo is then brought out to be questioned.

Agliè's group are, or have deluded themselves to be, the Tres society in the Plan. Angry that Belbo knows more about The Plan than they do, they try to force him to reveal the secrets he knows, even going so far as to try to coerce him using Lorenza. Refusing to satisfy them or reveal that the Plan was a nonsensical concoction, his refusal incites a riot during which Lorenza is stabbed and Belbo is hanged by wire connected to Foucault's Pendulum. (The act of his hanging actually changes the arc of the pendulum, causing it to oscillate from his neck instead of the fixed point above him)

Casaubon escapes the museum through the Paris sewers, eventually fleeing to the countryside villa where Belbo had grown up. It is unclear by this point how reliable a narrator Casaubon has been, and to what extent he has been inventing, or deceived by, conspiracy theories. Casaubon soon learns that Diotallevi succumbed to his cancer at midnight on St. John’s Eve, coincidentally the same time Belbo died. The novel ends with Casaubon meditating on the events of the book, apparently resigned to the (possibly delusional) idea that the Tres will capture him soon. And when they do, he will follow Belbo's lead, refusing to give them any clues, refusing to create a lie. While waiting, holed up in a farmhouse where Belbo lived years before, he finds an old manuscript by Belbo, a sort of diary. He discovers that Belbo had a mystical experience at the age of twelve, in which he perceived ultimate meaning beyond signs and semiotics. He realizes that much of Belbo's behavior and possibly his creation of the Plan and even his death was inspired by Belbo's desire to recapture that lost meaning.[6]

Most books written in this[which?] genre seem to focus on the mysterious, and aim to provide their own version of the conspiracy theory. Eco avoids this pitfall without holding back on the historical mystery surrounding the Knights Templar. In fact, the novel may be viewed as a critique, spoof, or deconstruction of the grand overarching conspiracies often found in postmodern literature. Although the main plot does detail a conspiratorial "Plan", the book focuses on the development of the characters, and their slow transition from skeptical editors, mocking the Manutius manuscripts to credulous Diabolicals themselves. In this way the conspiracy theory provided is a plot device, rather than an earnest proposition.

Belbo's writings are a recurrent theme throughout the book. The entire book is narrated in first person by Casaubon, with brief interludes from the files on Abulafia. These passages are often eccentrically written, and deal in most part with Belbo's childhood, his constant sense of failure, and his obsession with Lorenza. The interludes from his childhood serve as stark contrast to the mythical world of cults and conspiracies. Belbo is extremely careful to not try to create (literature), because he deems himself unworthy, although it becomes somewhat obvious that writing is his passion. This attitude of constant subconscious self-abasement fits in with the overall irony focused on in the book, considering that Belbo is eventually consumed by (re)creation of the Plan.

Casaubon is a scholar. While Belbo seeks inner peace, Casaubon's quest is of knowledge. The uncertainty of scientific knowledge and human experience is explored in his character, as he participates in various extra-natural events. His narratives abandon his strict realism and become increasingly inclined towards the supernatural as the novel progresses.

Mr. Garamond, whose primary business is selling dreams (through his vanity press outlet), comes to believe the fantasy world his authors weave. It is possible though, that he had always been a "Diabolical", and founded his publishing business to fish for information.

An obscure one-time reference to the fictional Cthulhu cult through a quote from The Satanic Rituals – "I'a Cthulhu! I'a S'ha-t'n!". The words closed a ritual composed by Michael Aquino. Originally just "I'a Cthulhu!", Anton LaVey added "I'a S'ha-t'n!" to give it a "Satanic touch".[7]

Foucault's Pendulum has been called "the thinking man's Da Vinci Code".[8] The parchment that sparks the Plan and its multiple possible interpretations, plays a similar role to the parchments in the Rennes-le-Château story propelled to global prominence by Brown's novel and, earlier, in The Holy Blood and the Holy Grail, from which Brown drew inspiration. Eco's novel, which predated the Brown phenomenon by more than a decade, similarly concerns itself with the Knights Templar, complex conspiracies, secret codes, the Holy Blood conundrum (if mentioned only in passing) and even includes a chase around the monuments of Paris. It does so, however, from a much more critical perspective: it is more a satire on the futility of conspiracy theories and those who believe them, rather than an attempt to proliferate such beliefs.

Asked whether he had read the Brown novel, Eco replied:

I was obliged to read it because everybody was asking me about it. My answer is that Dan Brown is one of the characters in my novel Foucault’s Pendulum, which is about people who start believing in occult stuff.

– But you yourself seem interested in the kabbalah, alchemy and other occult practices explored in the novel.

No. In Foucault’s Pendulum I wrote the grotesque representation of these kind of people. So Dan Brown is one of my creatures.[9]

Foucault's Pendulum also bears a number of similarities to Eco's own experiences and writing. The character of Belbo was brought up in, and refers to many times, the region of Piedmont in Northern Italy. In an article compiled in Faith In Fakes, Eco refers to his own visit to a Candomblé ceremony in Brazil, reminiscent of the episode in the novel, and also describes a French ethnologist, Roger Bastide who bears resemblance to the character of Agliè.[13]